The future of the entire Malcolm family:
Lois and Hal: Once again, they find themselves pregnant, but is it a boy or a girl?
Dewey and Jamie: Filling the void of Reese and Malcolm, Dewey and Jamie wreak havoc in the household much like Dewey, Malcolm, and Reese have done all these years.
Reese: Reese settles in happily as a janitor after taking Ida's advice, living with Craig.
Francis: Now that he has a job he loves much like Hal's, which he refuses to admit to Lois, he and Piama are happy together and plan on having kids soon.
Malcolm: Malcolm finally gains some happiness down at Harvard, however, he is also doing janitorial duties amongst other jobs to afford his tuition to reach Lois' dream of him becoming the U.S. President.
Only in the pilot episode is the last name of Malcolm's family made known. Francis calls home from the academy and the name tag he is wearing plainly says "Wilkerson" on it.
After Malcolm said to his parents "This is unbelievable, you actually expect me to be President?", he was holding a white towel in his right hand in the shot from behind, but after the next immediate shot, he wasn't holding any.
The family lives in California, as it as been seen on numerous episodes cars with the California license plate, which also explains why there was never snow and why it was so far a drive to Francis at military school.
When the family is sitting at graduation and there are no people sitting around them due to their smell, this is a reference to the first episode when no one will sit near Malcolm because he is smart.
When Reese and Craig are joining Malcolm, Dewey, and Jaime to burn the nuclear option, we see Reese and Craig carrying bags that say "Beds and Baths." This relates to the department store "Bed, Bath, and Beyond."
Reese tries to make a mess that will take 30 days to clean up, but instead he could have just made a huge mess on the 29th day, so they would have to keep him the extra few days.
When Malcolm name is being introduced for his graduation speech, his last name cannot be heard due to the microphone squeaking.
When Francis drops his employee card, on the card it clearly reads "FRANCIS NOLASTNAME."
When Lois opens the closet in the living room, it looks nice and clean inside and looks like a regular closet. But didn't they discover that in "Therapy" that the closet was a second bathroom?
One of the places Hal goes to while trying to get the contents of his wallet back is the Circus Burger, where Reese worked at briefly earlier in the series.
Caitlin Crosby, who plays Kelly, one of the popular kids in school also appeared in Season 5-2 "Watching the Baby." In that episode, she was Joanne, one of the 3 girls who went to Malcolm's house to ask him, Reese, and Stevie to the prom because their boyfriends ditched them. Ironically, that episode also involved the prom.
Hal tries to make Dewey happy about his childhood memory, so he created himself some artwork and pretended that Dewey made it in his first years in school to make him happy. Unfortunately, Dewey notices a picture of Grandma Ida without a leg and that she lost it a year ago, which refers to "Ida Loses a Leg."
This is the third time someone is saved by an animal(s) that is associated with Reese. Here, Craig was knocked down by a herd of cows (which were freed by Reese) just when he was about to make the biggest mistake of his life. The first is from Season 4-1 "Zoo," where Malcolm and Dewey were saved from being eaten by tigers when Reese threw the goat he was fighting with into the tigers' den. The next was Season 6-20 "Stilts," where Reese got too wasted from taking too many pills and stole a horse. It saved Malcolm from being beaten up by a former Lucky Aide employee.
This episode draws a conclusion to the long-running storyline of Craig's lovesickness towards Lois.
This is the final episode we get to see the Lucky Aide with Malcolm, Lois, and Craig working there.
Lois is still driving the old van, even though she won a new truck in the previous episode, "Bomb Shelter."
In this episode, Reese is back at his meatpacking job. However, in the previous episode, he becomes a telemarketer.
While Hal is reading the Playpen magazine, he once again expresses attraction for women with a little extra meat on their bones, the last time being when he was trying to make Lois gain extra weight when she was pregnant.
Malcolm turns out to be great at dancing even though Lois previously predicted that he would be a terrible dancer during an argument earlier in the series.